BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 045904
(296 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1YGP|A Chain A, Phosphorylated Form Of Yeast Glycogen Phosphorylase With
Phosphate Bound In The Active Site.
pdb|1YGP|B Chain B, Phosphorylated Form Of Yeast Glycogen Phosphorylase With
Phosphate Bound In The Active Site
Length = 879
Score = 29.3 bits (64), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 13/55 (23%), Positives = 26/55 (47%)
Query: 101 QTAMDADIRRKEAPASSRENSRGVSTQEWLEQRKRKIGKLLEANGLDTSRAYMLD 155
+T + D + P+ + G++ + WL+Q + KL+ D + Y+LD
Sbjct: 493 KTTIFKDFIKFYGPSKFVNVTNGITPRRWLKQANPSLAKLISETLNDPTEEYLLD 547
>pdb|2F9L|A Chain A, 3d Structure Of Inactive Human Rab11b Gtpase
pdb|2F9M|A Chain A, 3d Structure Of Active Human Rab11b Gtpase
Length = 199
Score = 29.3 bits (64), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 5/45 (11%)
Query: 200 EEYNRMKEADPEFYRGA--SSLQYGTAPKISEDKIERMVKELKDQ 242
E Y R+ A +YRGA + L Y A ++ + +ER +KEL+D
Sbjct: 65 ERYRRITSA---YYRGAVGALLVYDIAKHLTYENVERWLKELRDH 106
>pdb|2D7C|A Chain A, Crystal Structure Of Human Rab11 In Complex With Fip3 Rab-
Binding Domain
pdb|2D7C|B Chain B, Crystal Structure Of Human Rab11 In Complex With Fip3 Rab-
Binding Domain
Length = 167
Score = 28.9 bits (63), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 5/46 (10%)
Query: 199 LEEYNRMKEADPEFYRGA--SSLQYGTAPKISEDKIERMVKELKDQ 242
LE Y + A +YRGA + L Y A ++ + +ER +KEL+D
Sbjct: 64 LERYRAITSA---YYRGAVGALLVYDIAKHLTYENVERWLKELRDH 106
>pdb|2HV8|A Chain A, Crystal Structure Of Gtp-Bound Rab11 In Complex With Fip3
pdb|2HV8|B Chain B, Crystal Structure Of Gtp-Bound Rab11 In Complex With Fip3
pdb|2HV8|C Chain C, Crystal Structure Of Gtp-Bound Rab11 In Complex With Fip3
Length = 172
Score = 28.9 bits (63), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 5/46 (10%)
Query: 199 LEEYNRMKEADPEFYRGA--SSLQYGTAPKISEDKIERMVKELKDQ 242
LE Y + A +YRGA + L Y A ++ + +ER +KEL+D
Sbjct: 67 LERYRAITSA---YYRGAVGALLVYDIAKHLTYENVERWLKELRDH 109
>pdb|2GZD|A Chain A, Crystal Structure Of Rab11 In Complex With Rab11-Fip2
pdb|2GZD|B Chain B, Crystal Structure Of Rab11 In Complex With Rab11-Fip2
pdb|2GZH|A Chain A, Crystal Structure Of Rab11 In Complex With Rab11-Family
Interacting Protein 2
Length = 173
Score = 28.9 bits (63), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 5/46 (10%)
Query: 199 LEEYNRMKEADPEFYRGA--SSLQYGTAPKISEDKIERMVKELKDQ 242
LE Y + A +YRGA + L Y A ++ + +ER +KEL+D
Sbjct: 70 LERYRAITSA---YYRGAVGALLVYDIAKHLTYENVERWLKELRDH 112
>pdb|1OIW|A Chain A, X-ray Structure Of The Small G Protein Rab11a In Complex
With Gtpgammas
pdb|1OIX|A Chain A, X-Ray Structure Of The Small G Protein Rab11a In Complex
With Gdp And Pi
Length = 191
Score = 28.5 bits (62), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 5/46 (10%)
Query: 199 LEEYNRMKEADPEFYRGA--SSLQYGTAPKISEDKIERMVKELKDQ 242
LE Y + A +YRGA + L Y A ++ + +ER +KEL+D
Sbjct: 88 LERYRAITSA---YYRGAVGALLVYDIAKHLTYENVERWLKELRDH 130
>pdb|1YZK|A Chain A, Gppnhp Bound Rab11 Gtpase
Length = 184
Score = 28.1 bits (61), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 204 RMKEADPEFYRGA--SSLQYGTAPKISEDKIERMVKELKDQ 242
R + +YRGA + L Y A ++ + +ER +KEL+D
Sbjct: 81 RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDH 121
>pdb|1OIV|A Chain A, X-Ray Structure Of The Small G Protein Rab11a In Complex
With Gdp
pdb|1OIV|B Chain B, X-Ray Structure Of The Small G Protein Rab11a In Complex
With Gdp
Length = 191
Score = 27.7 bits (60), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 204 RMKEADPEFYRGA--SSLQYGTAPKISEDKIERMVKELKDQ 242
R + +YRGA + L Y A ++ + +ER +KEL+D
Sbjct: 90 RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDH 130
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.314 0.130 0.365
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,153,546
Number of Sequences: 62578
Number of extensions: 238106
Number of successful extensions: 381
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 379
Number of HSP's gapped (non-prelim): 9
length of query: 296
length of database: 14,973,337
effective HSP length: 98
effective length of query: 198
effective length of database: 8,840,693
effective search space: 1750457214
effective search space used: 1750457214
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.3 bits)